Abstract Biominerals have important functions in living organisms: apatite crystals are responsible for the strength of our bones and the hardness of our teeth, calcite and aragonite are used by many organisms for making shells, and magnetite and greigite help bacteria and birds to navigate in magnetic fields. In order to fulfill their roles in organisms, bio-minerals have strictly controlled physical and chemical properties. Transmission electron microscopy (TEM) is ideally suited for the study of the structures, arrangements, compositions, morphologies, crystallographic orientations, crystallographic textures, and magnetic properties of biominerals at the nanoscale. In this chapter, we review the state of the art in the application of TEM techniques to the study of these properties, both in biomineral crystals and at the inorganic-organic interface. Examples are taken primarily from studies of magnetic minerals that form in the cells of magnetotactic bacteria.